Confusion and Clarity
by xoc13
Summary: Bones realizes what Booth meant when he said he loved her.Story is complete.Rated T just in case.B&B.Summary sucks,just read.
1. Chapter 1

It was late and as usual Brennan was in her office working. Angela had tried to get her friend to leave early, but she couldn't. Brennan sat in her office trying to work on some case files she had neglected for a while. She knew that if she set her mind to it she could finish those case files, but something was bothering her.

Ever since Booth woke up from his comma he wasn't the same. She knew that he was hiding something, but not what. It was difficult for her to explain this irrational feeling she had. Logically she knows Booth is the same person, but the way he acts towards her tells her the opposite. She wants and needs to know what it is so she heads over to Booth's apartment ignoring that it is close to midnight.

She drives hurriedly to his apartment unsure as to why. She feels an increasing urge to get to him fast, like if she knows something bad is going to happen. She practically flew the distance from the Jeffersonian to her partner's apartment.

Desperately Brennan ran from her car to his apartment still unsure of why she had this urge. She knocked on his door fiercely. After what seemed like an eternity to her, Booth opened the door rapped in a towel.

"Bones, what's going on? Why are you so out of breath?" Although he was worried for her sudden arrival, all Booth could think about was how good she looked. Brennan, somewhat awed by her partner's toned muscles, only managed to say " I… uhm…" She didn't know why, but seeing Booth in just a towel and soaked made her hot.

"Bones what's going on? It's past midnight and you look weird." _But still a beauty_,he thought. "Sorry Booth, I should have waited until tomorrow to show up." She felt stupid for her unnecessary worry. He was obviously fine, _really fine_ she thought.

"No Bones it's ok. What is it that you have to tell me?" His gaze was a swirl of worry and confusion. "Booth, ever since you woke up from your comma I have felt that you are not the same. I'm not talking about you forgetting things like your socks or ties, but I feel that you are not the same with me"

Booth seemed confused, "What do you mean?" _Oh God_, he thought. _Does she know I love her?_ "Booth, I feel that you don't treat me the same way. You seem awkward around me. It feels like maybe you don't want to work with me anymore." Sadness spread through her gaze as she spoke the words.

Booth felt his heart sink, "How could you think that?" She stared heavily into his eyes without saying anything. He leaned closer to hug her and much to his surprise she allowed it. They held each other without much thought. Booth stroked her hair and as he did so he began to feel embarrassed. Her face redden too, but she couldn't move. She felt his erection on her. She was shocked and couldn't say anything. Both stayed still and couldn't move. Booth began to panic and pulled himself away. He put his hands on his crotch to cover his embarrassment. He began to say, "I'm so sorry Bones…I…" He thought to himself, _you idiot_. _How could this happen?_, and a little voice in his head told him, _OH, you know why._

Meanwhile, Brennan was shocked. She would have never imagined something like this could happen. She managed to speak out, "Booth, you don't have to be embarrassed. It is perfectly normal for males to have erections…", when it suddenly hit her that he loved her. _What? No! Booth doesn't love me, obviously he was sexually aroused…oh man, what am I saying this is Booth._

"Bones I am soooooo embarrassed right now…" _oh, way to go idiot._ " Bones I'm sorry if I upset you. I didn't mean it. Please don't think that I was trying to take advantage of you." "Booth I cannot believe it", without knowing how she suddenly had the answer she came to find. "Bones I already said I was sorry, and…"

Brennan's head was spinning in circles. She just couldn't make sense of it all. It was just too much. "I know why you are acting so strange. It's because you think you are in love with me." "Not think, I know." She saw the truth in his eyes and that just confused her even more. "Ever since I woke up I've wanted to tell you, but I just didn't know how. I was afraid that you wouldn't take it well, or that you would think that I was lost or confused. I'm not. It is very clear to me what I feel. I love you."

It was too much for her to process and all she could say was, "How could you do this to me Booth? How?"

Tears were forming in her eyes and as he took one step to wipe the tears, she took a step back. "I opened myself to you. How can you do this now?" Booth was unsure as to why she was reacting this way. "Bones it's not a joke. I love you and I want to be with you. I'm not going to leave. This is real."

"I don't believe it. For almost five years you kept us apart and now you want us together? How do you want me to take you in when I can't know for sure you will not change your mind and leave?" He felt her pain, "Bones, this is real. I'm not going to change my mind. I want to be with you, not just as your partner or friend, but as something more."

With tears down her cheeks, "I'm sorry but I cannot believe you. Not now." She ran out the door, and for a second he started after her, but decided it was best to let her calm down. He walked to his bedroom to put on some clothes now that his erection was almost completely gone.

She ran out all the way to the street without looking back to see if he was following her. In her desperation she didn't stop to check the road and ran into the street. The last thing she heard was a screech of tires and she felt the bright headlights of the car.


	2. Chapter 2

Booth sat in his living room looking at his cell phone. He wanted to call her so bad. He wanted to explain what he felt. Show her he wasn't lying; that what he feels is true. But he knew that it was best to wait until she had thought things out. Somehow he knew not to pressure her. His thoughts were interrupted by the sounds of sirens. They sounded pretty close. Soon the red and blue lights of the ambulance interjected through his kitchen window from the street. He didn't think much of it. _Probably an emergency call_.

A knock shrieked through the silence of his apartment. For a moment he got excited and thought it was Bones, his Bones, but he knew that it wouldn't be her. As the knocking continued, he walked towards the door. _Who could it be?_

"How can I help you officer?" "Are you Seeley Booth?" the officer asked. "Yes, I'm FBI Special Agent Seeley Booth. What can I help you with?" "There's been an accident out front. A woman was run down by a car…" _Bones_. "One of the neighbors told us that she is your girlfriend. That's why I came up here to notify you." "Where is she?" _This is my entire fault._ "The EMTs are loading her into the ambulance." Booth ran past the officer. He needed to get to her fast.

He arrived when the EMTs were loading her into the ambulance and hoped inside to go with her.

The ride in the ambulance felt like an eternity to him. _It's my fault._ One of the EMTs told Booth that she was in critical condition. He began to note the injuries to her body, primarily her head injury, but all Booth did was look at her. _Hang on tight. You are going to be fine._

At the emergency care Booth was impatient. It had been an hour since they had taken Bones inside and they didn't tell him anything. He tried to calm himself down thinking of how he could be of help. He then realized that he hadn't called anyone to let them know about Bones. He took out his cell phone and dialed Angela's number. "What the hell Booth? It's past two…" Angela spoke half awake, half asleep. "Angela, Bones was run down by a car and I'm here in the emergency care and they won't tell me anything. She didn't look good. I don't know what to do…" With a full voice now Angela sat up in her bed, "What? Tell me what hospital you are in so that I can go."

After a half hour Angela strode in the hospital looking for Booth. She found him slumped in a chair. "What happened to Brennan?" Booth barely spoke the words, "She was run down by a car…" _It's my fault_. "You already told me that. But why? What was she doing that she got run down?" A worried expression was now on her face. "Apparently she ran out into the street and she didn't see that a car was approaching…" Tears rolled down his cheeks. Angela felt remorse for making him feel bad, "Hey, handsome, it's not your fault." "Yes it is, we had a sort of argument and she ran out of my apartment and I should have gone after her but I didn't and then…" "Hey, don't blame yourself. How could you have known this would have happened?" _What were they doing in the middle of the night?_

The doctor came out, "Are you relatives of the patient?" Without thinking Booth jumped and said, "She's my partner." "And I'm her sister." _I had to lie_, she knew it was the only way to get information. "Follow me into my office."

"Most of the injuries from her body are just scrapes and bruises…" the doctor began. " Thank God, no broken bones or anything. What a relief." said Booth. Angela's expression ratified his statement. "Please let me finish. Although her body is fine aside from bruises and scrapes, the seriousness of her injuries lies in her head. During the impact she sustained several injuries to her head…" _oh god_, both Booth and Angela thought. "How serious is it?" it was Angela who found the strength to ask. "We can not know for sure until the results of her analysis are back, but…" _what?_ Booth shouted in his head. " I'm sorry to tell you this, but she has fallen in a deep comma." _Noooo_, Booth shouted once again in his head.


	3. Chapter 3

The next couple of hours would determine Brennan's fate. The doctors knew that every minute that she remained in that comatose state only endangered her life even more.

It was early morning when Cam, Hodgins, and Sweets arrived at the clinic. "What happened to Dr. B.", a frantic Hodgins asked. "When I got Angela's call this morning I was shocked. Both Sweets and Hodgins were at the Jeffersonian and we decided to head over here to see if there were any news." a worried Cam explained. "It's really hard to believe that Dr. Brennan is in a deep comma." Sweets' shock traveled through his words.

"The x-rays show trauma to her brain. The doctor told us that although her state is critical, she is fighting for her life. Oh…I just want my best friend to wake up."

"She's a strong woman. She will be fine. Ok. You hear me Angela? She'll be Ok." tears rolled down Booth's face. Everyone stayed quiet. No one could think of anything to say.

As the days passed, each of Brennan's friends took turns to watch over her. It was hard for the rest of the team to get Booth to go home and rest when his shift to watch her was over.

"Booth, you should go home. It's my turn to watch her, plus you will take the night shift again. Please go home and shower and rest. Nothing will happen to her while you are at home resting." As Booth made and effort to object, Cam raised an arm to stop him. She dragged him out of the room and got him to head over to his apartment.

At his apartment, Booth couldn't do anything but think about his Bones. He felt a deep pain inside his heart for letting something this bad happen to her. Although he didn't want to sleep, his body forced him to fall asleep in his couch. But even asleep he could only think of her. A smile spread over his face during his sleep.

_It was a nice warm day. He and Bones were out at a crime scene investigating a murder. He felt happy to have her by his side and doing what they do best. All he could do was smile at her. She caught sight of his smile and smiled back. Everything seemed so peaceful, but all of a sudden dark clouds covered the sky. Before he knew it she was gone. He ran to look for her, but couldn't find her. He yelled and yelled her name, "Bones!"._

Booth sat up and shouted her name, "Bones!". He needed to go back and make sure she was safe.

At the clinic nothing had changed. It had been a week since Brennan entered her comatose state and still no sings of recovery.

Booth strode into the clinic and practically ran to her room. He only slowed down when a nurse made a face at him for running inside the clinic. He felt a slight relief when he saw she was in her bed. Cam had fallen asleep. Booth tugged her awake to let her know he was taking over the shift. A tired Cam could no longer argue with Booth, and so she left the room.

Booth sat there looking at his Bones and praying for her to wake up. As night began to fall, Booth felt the need to lie down next to his Bones. He wanted her to feel that he was there. He fell asleep as soon as he was next to her on the bed. A nurse walked in and saw the peaceful sleeping man. "I wish a hunk like that would sleep next to me.", she said in a low voice before heading out the room.

As the lights of early morning began to arise, Booth was awakened by a groan. Much to his surprise the groaning came form Bones. He jumped out of the bed in excitement. _She's waking up_, he thought. After a few more groans, she opened her eyes. "Uhm… my head…" she was able to sound the words between groans. Booth was so happy she had woken up, that he couldn't stop smiling. "Bones what took you so long to wake up?". "What… happened? …Where …am I?" Brennan could barely ask. "You were run down by a car. You are in a hospital because you have been in a comma for a week now. But none of that matters now because you are awake now and …" he couldn't hold the urge any longer and kissed her. It was a gentle, but passionate kiss. As Booth trailed off, Brennan just starred at him and said, "Who are you?"


	4. Chapter 4

Booth had called the squints to tell them the news of Brennan waking up, though he did not mention her sudden amnesia. It was not long since they arrived at the clinic with a thousand questions in mind, but the expression on his face told them something was still not right. Booth explained that she had woken up and talked a little, but that she did not recognize him.

"Man, that sucks." Hodgins' words cut through the silence. "What are the doctors saying about her condition?" Cam was quick to point out her concern. "Nothing. They are still running tests." tears began to form in his eyes.

After about and hour of waiting, Brennan's doctor approached them. "I'm afraid the brain injury and her comatose state are the reasons for her amnesia. It is hard to say at this point how far back she remembers in her life or how long her amnesia will last. Time will tell us everything, but for now we can be grateful for her waking up."

Within a week Brennan was released from the hospital. She wasn't allowed to go back to the Jeffersonian for about another week or so. Angela visited her friend everyday in order to keep an eye on her. Brennan didn't remember anything from these past five years. There was so much she could not remember. The doctor had advised her friends to tell her things from her life, but to be careful as to how. The last thing she needed was to be overwhelmed with truths she didn't remember or could not understand. Angela was given the hard task of bringing Brennan up to speed with her life.

"Sweetie, I know this is hard for you and that's why we will take it slow and from the beginning. You don't remember anything from these past five years?". " I'm afraid not. I don't remember my so-called partner, Agent Booth. I don't remember this new boss, Dr. Soroyan or this FBI psychologist named Sweets. And I still can't really understand what you told me about Zack. I can't believe he is not my student anymore, logically I knew someday he wouldn't be my student anymore, but still. You know?" Angela tried to comfort her friend, "Give it time Sweetie."

"Ange… there's just so much that I lost. I mean… the only people I actually remember are you and Dr. Hodgins." a frustrated Brennan sighed. "All I want to do right now is get back to work so that I can't go crazy over this mess in my head. I'm physically okay and I can function as a forensic anthropologist quite well. I need to go back and work because I feel it's the only way I can regain my life back."

For the next two weeks Brennan was evaluated by her doctors and was found to be okay. Her head injury healed up satisfactorily, although her amnesia was still present. Cam had allowed her to return to work since she was heavily needed at the Jeffersonian and her doctors had approved her reinstatement. She was also evaluated by Dr. Sweets in order to determine if she was fit to work with the FBI. Sweets' evaluation stated that she was fit to continue her partnership with the FBI as long as she continued her sessions with him.

At the Jeffersonian, "Dr. Brennan it is good to have you back." Fisher greeted the doctor as she was heading towards her office. "Fisher, right?" she asked with a certain fear of getting the name wrong. "Yes, I'm one of your interns. I'll be here to help with this new case." "What new case? I was not informed of a new case." a hurtful expression began to form in her face for not being informed. "That's because the remains were just found. Agent Booth is waiting for you in your office so that you two can go visit the crime scene. I'm available if you need me to tag along." "Thanks, but I'll let you know."

She hesitated for a moment before stepping in her office. This was the first time she saw her "partner" since she woke up. "Good morning, Agent Booth. Fisher just told me about the new case and I'm ready to leave when you say so." Booth looked hurt at her greeting. "Bones you usually call me Booth." "I'm sorry, but I can't remember certain things…" _a lot of things_, "but I'll make sure to make a note of that…Bones?" "I've called you Bones since we began as partners, but if it makes you uncomfortable I will not…". "That's not necessary. You can still call me Bones. I need to regain my life back and this seems like a good start. Are you ready to go?" _Yes, a good start; a new beginning. Perhaps this is my chance of making her mine and explain how I feel_, Booth trailed in thought as they headed towards the crime scene of their new case.


	5. Chapter 5

The ride to the crime scene was quiet. Tension and awkwardness was heavy in the car's atmosphere. Booth hated the silence and tried to make conversation, but every time he opened his mouth he couldn't speak. Brennan was quiet. She wanted to break the silence, but couldn't find the words. Before they knew it they arrived at the scene.

"Female; late teens early twenties." Booth watched in awe as his Bones conducted her examination of the remains. He couldn't believe how good she was. He felt sadness at the thought of her only forgetting him because she wanted to. "The probable cause of death is blunt force trauma to the skull… Are you listening Agent Booth? I'm sorry, Booth." Brennan was aware of his lack of attention. "Of course Bones, female in her late teens or early twenties and got conked on the head." he said giving her his charm smile. Unknowingly she returned the smile and he felt relieved at her expression.

At the lab it was easy for Angela to do a facial reconstruction. Her sketch found a match and she hurriedly gave her results to Brennan. "Her name is Dinah White, 20. She was reported missing last week." "Thanks Angela. Someone should inform Agent Booth." "That would be you Sweetie." "Right, I will inform Agent Booth." As Brennan began to walk out of her office she was stopped by her friend's arm. "Sweetie, you need to stop being so weird around Booth. It breaks his heart that you don't remember him, but not wanting to talk to him will kill him." "It's not that I don't want to talk to him… it's just that I don't know what to say." " Brenn, just talk to him like you talk to me and you will see how much easier that makes it." "I will."

Brennan called Booth to inform him of their victim's identity. She and Fisher had examined the remains, but beside her fatal head injury there wasn't much else to look at. She was in her office waiting for Booth to show up. _Since when did I begin to miss him?_ Angela's voice interrupted her friend's thoughts. They began to head out of the office when Brennan stopped. She saw Booth out in the platform. "Hot", Brennan said the words without thinking. "Sweetie?" Angela said in shock. "What?" a confused Brennan replied. "You just said 'hot', and are you starring at Booth?" Angela could not believe her eyes. "Oh, yes. He is totally hot." Angela dragged her friend deeper inside the office, almost out of sight and said, "You are checking him out. You have the hots for your partner. You like him and I don't even know if to jump or cry. I have been trying to make you admit you like him, but why now?" "If you have been trying to get me to admit it for so long, then why are you so worried?" "Don't you see? If you let your emotions drive you right now and you tell him how you feel and then you just ditch him, you will break his heart and he will die of sadness. He loves you Brennan and you can't ignite his feelings if you are not certain of what you feel." "Angela, I just said he was hot. That's it." "Look, you can lie to me, but you can't lie to yourself. Think about it before you try to take a step forward. Please?" "Don't worry Ange, I will."

A few days had passed and Booth discovered that the victim's stepfather had a motive and the opportunity to kill her. Booth knew that the stepfather's house was only a few miles from where they had found the victim. It was him. There was no doubt.

"Bones, we gotta go check out the stepfather. I think it might have been him. Come on, his house is in the middle of the woods were we found the victim. We gotta go." "Just let me get my jacket."

They were headed to the suspect's house and the ride suddenly became quiet. "Seems like it's going to rain." it was Brennan who cut through the silence. Booth was glad that she was the one to start the conversation. "Don't worry Bones, we won't be much in the rain." And once again silence filled the car. Brennan sneaked peaks at him and thought to herself, _I could just eat him up. Temperance what are you saying? He's your partner._ "We are here Bones." "This house is so far out from any communication. It's ideal for someone to commit a murder with no one around." "Yeah, and it's too quiet. Please stay near me."

They approached the house and found that the front door was open. It was like if he was waiting for them. They crept inside carefully and found no one. A loud shot was heard behind them and Brennan instantly jumped and grabbed Booth's hand. He felt her soft had clenched his. "It's okay, but I need you to stay close." They headed towards the front door again and heard yet anther shot. Booth knew that someone was hunting them. When they got outside he saw that someone had messed with his SUV's motor and there were two shots in the hood. "Son of a bitch. Where are you?"

The rain began to pour heavily and Booth knew that hiding in the woods was not a good idea, but it was the only choice. They began to make their way through the trees when shots came behind them. Booth pulled Brennan so that she ran at his same speed. He heard her groan and saw that she was hurt. "Bones! Where did he get you?" "My leg, but I'm fine. It's just a flesh wound. We have to keep running."

Running through the forest was hard enough without adding the mud produced by the rain. Without knowing it they slipped and fell into a ditch. Booth landed on his side and was just left without air, but Brennan hit her head on a rock. Through her dizziness Brennan warned Booth of the man standing behind them. In an instant Booth turned around and shot the man in the chest. He fell between the both of them. Worried that he might not be alone in their hunting they got out of the ditch and ran.


	6. Chapter 6

The storm grew heavier and they couldn't run anymore. Brennan was the first to stop. Booth turned to face her and asked, "What's wrong?". "It's weird, but when I hit my head back in the ditch…" "Are you hurt Bones? I don't see any blood on your head…" "I'm not bleeding from my head. When I hit my head I suddenly remembered all these years. It's weird, but in an instant I remembered all that I had lost." "That's great Bones. I'm really happy that you are you again." "Booth? I think we should get out of the rain. That man is dead in the ditch and we are far away from the ditch. It's best if we find a place to pass the night and when morning comes we can find our way out." "Yeah, Bones. That's a good idea."

They searched for a place to pass out the storm and Brennan pointed out a waterfall. She lead the way and found that there was a rock opening behind the waterfall. They climbed inside soaking themselves one last time before being inside. The space was reasonable for the two of them. They could easily spend the night there without discomfort. " Wow Bones, good eye. You found us a good spot."

"We should get out of these wet clothes before we catch pneumonia." Brennan's voice echoed. "What? No! We don't have any other clothes to change into." " Booth this is no time to be shy. If we don't get out of these clothes we will get sick and probably wont make it throughout the night. Look, if it's because of what happened when I had my accident…" "Bones! I'm not gonna be naked in front of you. What if you know what happens again? I don't want you to run out again and conk your head and get amnesia. No!" "Booth! I'm sorry that I reacted so childish that day, but I didn't expect that to happen. I was shocked at realizing how you felt for me and I'm sorry if I hurt you with my reaction." " You don't have to apologize. It should have been me who should have had control over… well… you know." " Booth you gained my heart with your respect. And I have to say that… I not only love you too, but… you make me hot too." she threw a sexy smile at him. "Bones!" his face got red. "What? It's the truth. And you know… seeing you all soaked makes me…" she leaned closer to him and gave him a kiss. He allowed her to kiss him and he placed his hand on the small of her back. "Bones…please don't." he said as he pulled away. "Why?" she was confused. He allowed the kiss, yet he wanted her to stop. "Because I know it's not going to happen and if it doesn't happen I'm going to die and…" she leaned even closer and whispered into his ear, "You are not going to die before living this with me."

She kissed his neck and followed to his mouth. Their kiss was full of passion and yet it remained pure. She pulled away from him and stood. She pulled her shirt off and then slid her pants down. She enjoyed his hungry look as she undressed. He was in awe of her beauty and he remained seated looking up at her as she undressed. She was now in her underwear and braw. She teased him a little before removing her braw. He was now ready to jump and eat her in a passionate kiss, but he remained seated as she undressed. She removed her panties slowly, as if to give him a chance to enjoy the view. When fully undressed she walked towards him and gave him a sexy look. She sat down next to him and he understood what her eyes were saying. _Take it off_. He stood obediently and began with his socks. He unbuckled his belt and slowly took it off. Shivers ran through her as he took off his shirt. His pants fell fast to the floor. He couldn't wait any longer. As he took his boxers off, Brennan stood up and pulled him towards her. Their kisses were fierce and they held each other closer with each kiss. He kissed all of her body; there was not a spot left of her that his lips hadn't kissed. He carefully caressed the spot the bullet had left its mark. It was just a scratch, but he wanted to soothe her skin. She pushed him to the floor and got on top of him. She teased him for a while before allowing him to slide inside her. Their night was full of passion and love. They finally allowed themselves to have and enjoy what they yearned for so long.

When the morning came, they were holding each other tight. The heat of their passionate love making kept them warm through the night. It was time to head back and return to their lives. Both were afraid that the other had changed their mind about their encounter, so they held each other tighter without wanting to let go. Brennan was surprised to feel that his hands were no longer on her back. She blushed as she felt them slide underneath her. His hands rested on her breast and he began to kiss her neck as he made his way to her breasts. She then knew that what they had shared was not a one night thing and that when they would go back to D.C. they would do this again and again.


End file.
